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Old 11-29-2012, 11:39 PM   #1
abh
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Location: philadelphia

Join Date: Aug 2012
Posts: 13
Default Tophat with bowtie2

Hi,

I want to align the Rna-seq data using bowtie2.so here are the steps i did(i installed tophat,bowtie2 and samtools and kept in bashprofile)

i got the reference genome from bowtie2(hg19) and i ran the makescript for indexing them.i got
6 index files(hg19.1.bt2 hg19.2.bt2 hg19.3.bt2 hg19.4.bt2 hg19.rev.1.bt2 hg19.rev.2.bt2)and i kept in genome folder hg19

now i want to run the tophat by takine these index files and the fastq file like this but i am getting error
[ab RNASEQ]$ tophat /net/gs/vol3/shared/lab/RNASEQ/hg19/hg19 C_RNAseq_1.fq

[Thu Nov 29 23:45:21 2012] Beginning TopHat run (v1.4.1)
-----------------------------------------------
[Thu Nov 29 23:45:21 2012] Preparing output location ./tophat_out/
[Thu Nov 29 23:45:21 2012] Checking for Bowtie index files
Error: Could not find Bowtie index files /net/gs/vol3/shared/lab/RNASEQ/hg19.*

can anyone help me with this?i am new in using the tophat

Thank you
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Old 11-30-2012, 12:30 AM   #2
mknut
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Location: UK

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Posts: 23
Default

It looks like tophat thinks that your index is in
Code:
/net/gs/vol3/shared/lab/RNASEQ/
not
Code:
/net/gs/vol3/shared/lab/RNASEQ/hg19/
. Try moving your index to a folder that does not include "hg19" in its name - it seems to be confusing tophat. Say
Code:
/net/gs/vol3/shared/lab/RNASEQ/my_index/
should do the trick.

EDIT: It looks like I did not notice the elephant in the room - you are using TopHat v1.4.1 which does not support Bowtie 2. Use Tophat version >2.0. From TopHat website:
Quote:
Version 2.0.0 is a major release adding Bowtie 2 support

Last edited by mknut; 11-30-2012 at 12:53 AM. Reason: misread the question
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Old 11-30-2012, 02:39 AM   #3
masterpiece
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Location: malaysia

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Default

Quote:
[Thu Nov 29 23:45:21 2012] Beginning TopHat run (v1.4.1)
You cannot run tophat 1.4 with Bowtie2. You have to install Tophat version 2.0.* if you want to use Bowtie2.

kamal
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Old 11-30-2012, 09:06 AM   #4
abh
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Default

thank you

Its working now
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